Under Jolly Roger
by xXdreameaterXx
Summary: When the Doctor, a renegade from the Royal Navy and pirate and captain of his beloved ship, the TARDIS, picks a woman called Clara from out of the sea, he soon realizes he might get more than he bargained for. Clara is not only a feisty woman, but also very pretty and he starts to regret the promise that he made her, to let her go once they have reached the next harbour. PirateAU
1. Chapter 1: Man Over Board

_This is what happens when you have to entertain yourself with interesting thoughts while at work. This fic will have 3 chapters._

 _Explanations, for those who need them:  
\- The "Jolly Roger" is the name of the skull and crossbones flag flown by pirates ships. "Under Jolly Roger" is also a song by the band Santiano, which I love (check it out!)  
\- "German duke" refers to King George I who came to be on the throne of Great Britain and Ireland because the Act of Settlement didn't allow Catholics to reign and the Duke of Brunswick-Lüneburg was Queen Anne's closest protestant relative. The Jacobites unsuccessfully tried to dispose of him.  
\- The "steersman" is the man that steers the ship  
\- A "skiff" is a small boat.  
\- A "jolly boat" is also a small boat. Here it's the term for a boat used by the crew to go on shore and back to the ship._

 ** _Under Jolly Roger_**

 **Chapter 1: Man Over Board**

The waves were gentle tonight and a soft wind was blowing them exactly where he wanted his ship to go, so the Doctor settled in his bunk and closed his eyes. It would be a while until he could feel solid ground under his feet again but his crew was in a good mood about it now after their shore leave. They had spend a whole weekend drinking and whoring and the Doctor smiled at the thought of it. Back in the old days, when he had still been a captain in the Royal Navy, he had had a lass in every harbour, promising each of them his hand in marriage before leaving to do his duty for King and Country. Now he was getting old and grey and the twin hearts tattooed on his chest were already fading, but the Doctor knew that wasn't the reason why fathers dragged their daughters away from the window whenever they stepped ashore. It was his men's tattered uniforms and the black sails of his ship.

His ship had been and always would be his one true love. The _TARDIS_ had never once let him down and even though her blue paint was beginning to crumble away here and there, she was still bringing him safely through every single storm. The Doctor had stolen her, of course, the best ship in the King's entire fleet, at least in his opinion. He had always been unhappy in the Navy, hating to obey orders but he'd be damned if he died for a German duke that had no place on the throne of Great Britain.

The Doctor's hands trailed over his bare chest, outlining his old tattoo and he wondered if he should have it renewed. One heart to pump blood through his veins, another to give to the sea. Ever since he had been a little boy the sea had been calling out to him, and so far the call hadn't stopped. He hated spending time ashore and whenever his fellow sailors complained about sea sickness or dizziness because the floor beneath their feet never stood still, the Doctor only laughed at them. He lived for it, the kind of freedom only the salty sea air, a ship and the wind in his sails could offer.

" _Man over board!"_

The words tore him from his dream and the Doctor sat up straight. These words were usually the beginning, the words that added a new member to their crew. They picked up stranded people here and there, saving them from ship wrecks or wherever they had come from and once they had gotten a taste of the pirate life, only few of them wanted to leave again. The Doctor rose from his bunk, quickly threw his coat over his shoulders and slowly made his way up to the deck.

His crew had gathered on the starboard side of the ship, leaning over the railing to look at the water.

"What's going on?" the Doctor demanded to know, "Who told you all to abandon your posts?"

Some of the crew members quickly hurried off, back to work. The sea never slept, not even when it was dark and the moon and stars were so clearly visible in the sky like they were right now.

The steersman came to a halt next to him as he made his way back to the wheel. "Captain, there's a man in the water. In a skiff."

The Doctor retrieved his spy glass from the inside pocket of his jacket and looked out onto the water.

"I believe you will need to have your eyesight checked next time we step ashore, steersman," the Doctor snorted, "That's not a man. That's a woman. Ready the jolly boat!"

"But captain-" another crew member objected. He was a young lad in his 20s and the Doctor couldn't remember his name if his life depended on it. "It's bad luck to have a woman on board."

"Can you read?" the Doctor asked back, staring down at him with his eyebrows knitted. He knew that this look on him intimidated the younger crew members.

"Y-yes," the lad spluttered.

The Doctor pointed to the large plague next to the door that led inside the ship. "Can you read what that says?"

" _The Captain's w-w-word is law._ "

"Good we've cleared that up. Now bring me that woman. She's too far away from the nearest shore and if we don't help her, the next person to find that boat will also find a corpse."

It took the lad and two other crew members half an hour to bring the woman on board of the TARDIS and the Doctor watched the entire scenario through his spy glass, chuckling as he did. The lass was struggling, obviously not very keen on being saved by pirates and after she had slapped two of his men, the Doctor couldn't wait to meet her. She was undoubtedly a spirited woman and feisty, something he welcomed greatly. The days on a ship could feel long, it was good to have entertainment.

"Let me go!" the woman shouted when they had finally brought her on deck, still struggling against his men's grip, "I swear to God I will kick you in the balls."

The Doctor stepped up and chuckled. "Let her go," he told his men calmly, "I doubt she'll run very far."

When she was finally free the woman stepped closer and came to a halt right on front of, staring at him angrily. The Doctor had almost laughed out loud because she was so tiny that he was sure he could just lift her up and carry her to the cells below deck if she annoyed him too much. Apart from her size she was a truly bonnie lass with big, dark eyes and brown hair dishevelled by the wind.

"I demand that you put me back in my boat and leave me alone!"

Now the Doctor laughed indeed. "Lassie, you're more than a day's journey from the nearest land, that is if you have a ship with large sails and favourable winds. You'll die of thirst long before you will even see land in that boat of yours. Where were you even trying to go?"

"Away," she spat.

"Oh, how convenient," the Doctor chuckled again, "That's exactly where we're going. What's your name?"

"Clara," she replied angrily, crossing her arms in front of her chest.

"Well, Clara, I'm the Doctor, the captain of this ship and I welcome you as our guest until we've landed in the next harbour."

"Which harbour?" she demanded to know.

He shrugged and granted her a mischievous smile. "I don't know yet. I love surprises, don't you?"

"I want-"

The Doctor silenced her by placing his index finger over her lips.

"Let me finish that sentence for you. You want dry clothes, something to eat and a bed in a private cabin. Follow me."

He led the way and knew Clara was following after him by the sound of her unsteady footsteps and the muttering of curses. He was curious to know her story, know how she had come to be in that small boat in the middle of the ocean and what she was running from. And she _was_ running, the Doctor knew that look on her face too well to mistake it for anything else, for he saw it every time he looked into the mirror. One other thing he knew for certain: the following days on board would be anything but boring.


	2. Chapter 2: Under My Protection

_Awwww, thank you for the first reviews. I think it's going to be 4 chapters instead of 3 – and I'm not sure I can update the next two days, but I'll try. Also – Hippie AU starts on Sunday (definitely!)._

 _ **Chapter 2: Under My Protection**_

After being shoved into a small cabin, Clara took her first deep breath ever since she had been captured by the pirates. The captain could speak about saving her and being their guest as much as he wanted, Clara only knew that she was not here on her own free will. The Doctor had told her to put on some dry clothes and then meet him in his own cabin for dinner before he had sneered at her. Clara disliked him – but she also had an idea.

She had managed to escape once before, not from pirates, but from her own husband who she hadn't even wanted to marry in the first place. It had been so easy to sweet-talk him into drinking more and more of the wine served at their wedding and he had fallen asleep the moment his head had hit the pillow. All Clara had to do was climb out of the window and steal the first boat she saw, hoping that some merchant ship would pick her up and bring her to wherever she wanted to be. She would have told them a story about having been kidnapped and escaped (not entirely true but close enough) and begged them with her puppy dog eyes to take her to London. However Clara had the feeling that these pirates would not be fooled so easily and she didn't want to spend more time on this ship than absolutely necessary. And once she had stolen the jolly boat and was found by merchants, she could tell them a real story about having been kidnapped by pirates.

Clara opened the large chest in the back of the cabin and realized that she wouldn't find any kind of dress that she was used to, so she settled for a pair of brown trousers, a plain shirt and a vest. She searched the chest for something that could be used as a weapon but found nothing of use and so she closed it with a loud _bang_.

The captain's cabin was as dirty as the rest of the ship, but at least it smelled nicer like freshly blown out candles.

"Hope you like fish," the Doctor said as he pointed to the empty chair in front of him, "It's not like we get much else out here."

With a shrug Clara sank down in her seat and watched as the Doctor poured them both a glass of wine, providing her with the first requirement of her escape plan.

"So, Clara, what's your story?" the Doctor asked, sipping his wine.

She stared back at him. "What's yours?"

The Doctor huffed. "You're not making this easy for me, are you?"

As he rose from his chair to go through a small cupboard behind him, he provided Clara with yet another requirement. When his back was turned towards her, she quickly reached for her glass and poured the contents on the wooden floor where the wine swiftly disappeared in the cracks. A few seconds after she had set her empty glass back on the table, a handful of medals hit the wooden surface with a clang. Judging by the amount the Doctor was obviously a war hero of some sort.

"I'm the son of a Scottish fisherman. As soon as I could I joined the Royal Navy. I didn't like it very much," he nodded towards the medals, "And then I stole a ship and ran away. I'm still running. Your turn now."

"Could I have some more wine?" she asked him boldly.

The Doctor's eyes wandered from his own glass to her empty one and finally settled on her face. He looked at her so intently that for a moment Clara thought he had figured out her plan but eventually he reached for the bottle and filled both of their glasses to the brim.

"I ran away, too," Clara confessed after the Doctor had sat back down and taken another large gulp. This would be easier than she had originally thought, "From my husband."

"Why? Did he beat you?"

"No, I just didn't want him," Clara said plainly, "I was hoping for a ship to pick me up and bring me to London."

"We're not going to London," the Doctor replied and turned his back to her once more, pointing at the ocean through the window, "This is where we're going. The vast and dangerous and beautiful sea."

Clara used his moment of distraction to empty her glass on the floor once more, leaving only a small sip. When the Doctor turned back towards her, he looked at her in surprise and chuckled.

"You drink like a sailor, Clara. Are you sure you don't want to stay? I could see you fit in nicely."

"You don't drink like a sailor," she said provocatively and smiled, "And no, I'd rather you dropped me off next time you land in a harbour. Any harbour."

To her relief his finished his glass and immediately refilled it. "See, I'm afraid that's gonna be a long time. I haven't seen Spain in a few years. I kinda miss it. Have you ever seen Gijón?"

Clara was furious and about to yell at him but she managed to hide her anger behind a smile. She would never end up in Spain because she would leave this ship tonight and nothing, not even the Doctor, was going to stop her.

"No, can't say that I have," she replied politely. Under normal circumstances she would have loved to travel the world, but being held prisoner by pirates were not normal circumstances.

"I'd _loooove_ to show it to you," the Doctor said, slurring a little. He really didn't drink like a sailor if three glasses of wine were enough to get him drunk. He was almost making it too easy for her, "The Spanish dance like the _devil_."

"Oh?" Clara asked, watching him finish his drink.

"Aye, but don' tell 'em that," he hiccuped, waving his hands in front of her face, "I was wanted by the In-qui-sition for sayin' so."

When the Doctor leaned back in his chair and started yawning, closing his eyes in doing so, Clara poured her wine on the floor again. Soon he'd be out cold and she would be gone long before he woke up.

"Hey, how about some more wine, mh?" Clara prompted him with a smile and the Doctor seemed more than happy to oblige and after only two more gulps his head finally hit the table and he started snoring.

Clara almost started giggling when she heard the sweet sound that promised her her freedom and quickly she gathered the remainders of their dinner up in a clean cloth and headed out of the cabin. The ship was dark and almost eerily quiet, the sound of the creaking wood beneath her feet betraying her presence – if anyone listened to it at all. Just a few more steps and she would reach the jolly boat. Three, two, . . .

"Where do you think you're going?" a voice behind her suddenly asked.

Clara shot around and immediately recognized one of the men who had brought her on board in the first place. His teeth were rotten and she could smell the stench of him already. For someone who lived so close to a clean source of water he surely didn't use it often enough.

"Just. . . having a look around," Clara shrugged, hiding the bundled food behind her back.

The man stepped closer, sneering at her through his stained teeth and Clara was close to vomiting but she was too scared of what would happen if she ran from him.

"Does the captain know?"

"Of course," she lied, trying not to show how frightened she was, "He said I could go wherever I wanted before he went to sleep."

"Asleep, huh?" he came to a halt right in front of her. Clara didn't like the way he looked at her but she saw all of her escape routes blocked as he cornered her, "Good. You and me, we've got a score to settle."

Clara swallowed hard when he suddenly pushed her against the railing with the weight of his body, the physical contact disgusting her but as she tried to struggle free of his grip she found him resisting.

"No, you won't get away this time. You bit me when I brought you here and I'm gonna bite you back," he cackled and he was close to pressing his mouth against her own when suddenly she heard the click of a pistol.

"Step away from her," the Doctor ordered and when the man realized who was standing behind him, he quickly distanced himself from Clara.

"Sorry, captain. She was wandering around the ship. I just wanted to make sure she's not up to mischief."

"Clara is under my personal protection," the Doctor said sharply, "The next man who touches her walks the plank. Is that understood?"

"Yes, captain," the man nodded and quickly hurried off.

"Be sure to tell the others," the Doctor called after him before he came to lean against a mast, observing Clara closely.

As grateful as she was for being rescued, she wasn't sure she understood how and why.

"You're not asleep."

The Doctor snorted. "Clara, did you really think a few glasses of wine would knock me out? _Please._ Don't insult me."

"Then why did you-" she broke off, realizing that he had indeed seen through her plan from the very beginning. He had even made sure she would have enough time to pour away the wine. It all made sense now.

"I was curious," he admitted with a shrug, "You obviously wanted _something_ and I was curious to see what you'd get up to if you thought no one was watching. And let me tell you, it's a stupid idea."

Clara crossed her arms in front of her chest.

"You'll die out there on your own. The shore is too far away and there aren't many ships sailing these waters. Whether you like it or not, we're your best chance."

"Will you really let me go once you've anchored somewhere?" she asked him.

"I said that, didn't I? Do I not look trustworthy enough to you? After saving you twice?" the Doctor looked a little hurt, but Clara guessed that was as much of a play as him pretending to be drunk.

"I don't seem to have much of a choice other than trusting you," she realized.

The Doctor granted her a smile and it was the first thing she saw on his face that she thought was real. "Right. Now go to sleep. You won't get much once the rest of the crew wakes up."

With a sigh Clara followed him back inside. So her first escape plan had failed and now even she had to admit that it hadn't been a very good one to begin with. While most of the crew seemed disgusting and vile, she felt relatively safe when she was around the Doctor, so she guessed it could have been worse. Yet Clara was still determined not to stick around any longer than until their next shore leave.


	3. Chapter 3: An Escape Plan

_Thank you soooooo much for the reviews. I'm also upping the final chapter count of this to 6 (grumbles unhappily cause this wasn't planned but I'm hopeless against the muse)._

 _ **Chapter 3: An Escape Plan**_

One week. It had been one week since her capture and Clara was beginning to come to terms with it. After all, she had to admit that it could have been much, much worse. Even though he never really left her out of his sight the captain was nice to her and if he kept his promise to drop her off at the next harbour they anchored in, everything would turn out fine. Clara hated to admit it but the Doctor was a clever man and she had even come to respect him for that. What she hated even more to admit was that he was kind to her and by now it had also rubbed off on his crew.

After the encounter with Pit (she had later learned his name) on her first evening on board and the Doctor's threat all of the crew members had been exceptionally nice to her and she had even found ways to make herself useful and pass the time. That was how she stormed into the Doctor's cabin in the morning, bringing him breakfast and opening the curtains.

"Rise and shine," she said happily as she placed the tray on his table.

She was met with a loud and annoyed groan coming from underneath the blanket that made her giggle.

"Have you been indulging in the rum again?" Clara asked him, laughing lightly.

"I'm a pirate," he replied, struggling into a sitting position, "That's what we do."

"Well, your head clearly isn't thanking you," she remarked and was about to make her way back to the door when the Doctor reached for her arm. For a pirate his touch was surprisingly gentle and it didn't fit into the picture she had had of pirates before.

"Sit with me," he told her calmly, "For a moment."

After hesitating briefly Clara followed his order and sank down on his bed. She was quite astonished to find it so soft.

"You seem to get along well with my men," he began.

"Well, you did threaten them with the plank."

" _And_ you're seaworthy. The waters we crossed so far are rough and you haven't complained once. I've seen grown men throw up while sailing these exact waters. I'm quite impressed," the Doctor gave her an odd smile and suddenly it dawned on Clara what he was trying to do.

"You promised to let me go once we've reached a harbour," she reminded him calmly but inside she was panicking. What if he broke that promise? What if he did sail all the way to Gijón? What if he locked her up in her cabin until they had left for the open sea again?

The Doctor's smile didn't fade and only now she became aware that he still had a grip on her arm. Carefully she pulled away from him.

"I know what I promised you and I won't hold you against your will. I just thought you might change your mind and stay for a while longer. After all, it's not like you have anywhere in particular you need to be."

He was right. London had just been an idea and Clara didn't know what she would do once she was actually there. But these people were pirates, not the kind of company a lady like her should keep and even though they seemed nice at the moment, it didn't mean they always would be. No, she was better off far away from them.

"Thanks for the offer," Clara replied kindly, "But I'm a landlubber."

"Alright," the Doctor sighed and made an attempt to get out of bed when Clara suddenly thought of another question that had been on her mind ever since she had first seen the Doctor without his shirt.

"What does your tattoo mean?" she asked him and the Doctor looked back up at her, seeming a little puzzled.

"Uhm," he paused, "I always say: _One heart to pump blood through my veins, another to give to the sea_."

Clara cocked her eyebrows. "Haven't you ever met a woman worth giving your heart to?"

"Many," the Doctor replied, "But I'm a sailor. It takes a special kind to woman to pack up her entirely life and sail the oceans with me."

"Yeah, you're probably right," she agreed.

When Clara stepped on deck she was greeted by a familiar song, one of the shanties the pirates have been singing all week during their morning routine and Clara smiled at the sound of it and quickly joined in as she went to pick up a few stray items that the wind had blown all over the place. She said good morning to everyone in passing and finally came to a halt next to a group of men gathering around the wheel.

"What's up?" she asked them curiously, "What are you all looking at?"

"Nothing that should concern you," the steersman replied grumpily and Clara had almost sighed. He was the only man on board not really keen on her presence, not cause he disliked her personally but because he was one to believe that a ship was no place for a woman. The fact that Clara wasn't even here on her own free will didn't seem to matter much to him.

"How often do I have to remind you that Clara is our guest and you will treat her like any other member of the crew while she stays?" the Doctor asked as he stepped up to the wheel, the annoyance all too audible in his voice, "Now tell us the news."

"Captain," the steersman cleared his throat, "There is a ship, merchants by the looks of it. We saw them through the spying glass, they're sailing south west and they haven't spotted us, we think."

"Interesting," the Doctor mused and retrieved his own spy glass from his pocket to have a look. It seemed to take him a while but eventually he appeared to have spotted the ship.

"Same procedure as always?" the steersman asked him.

"Almost," he replied and suddenly turned towards Clara, "Do you fancy a little trip?"

"Me?" Clara asked in surprise, not sure she fully understood, "Why? Where to?"

"To the merchant ship, of course," he granted her a mischievous smile.

For a moment she was too lost for words to say anything. Was he offering to let her go?

Again the steersman cleared his throat. "I think we should send Johnny like we always do."

"No offence, but ever since Johnny lost his eye people have become wary of him. I say we send Clara."

"To do _what_?" she demanded to know.

Finally the Doctor looked back at her and retrieved another thing from his pocket. "We're pirates, Clara, we want to steal anything we can from this merchant ship. We would put you on the jolly boat and you'd pretend to have survived a shipwreck. They'll take you on board and at dinner you'll slip this," he held up a little vile, "Into their food or drink."

"What is it?"

"A sleeping drought. Will knock them out for a couple of hours and once you've given us a sign we will board the ship, take what we can and we'll be long gone by the time they wake up."

Clara couldn't help but laugh. Somehow she was having trouble believing that he was serious about this. "Don't pirates usually fire their cannons and board other ships by force?"

"We're not normal pirates," the Doctor explained with a smirk before his features froze into a stern frown, "And I'm not so fond of bloodshed."

"But you fought in the Royal Navy," she argued.

"Doesn't mean I liked the fighting. Now, will you do it or shall we send one-eyed Johnny in the hopes that they trust him anywhere near their dinner?"

Clara sighed. It was a risky move but she could do it. She could get away, have the merchants pick her up, warn them about the pirates. The Doctor was practically offering Clara her escape on a silver plate, so why did it feel so wrong?

"I'll do it," she finally agreed, swallowing the doubts gathering in the back of her head. Soon, with the help of the merchants, she would be back on the island.


	4. Chapter 4: Trust

_Uhhhh, thank you guys for the reviiiieeews :)_

 _ **Chapter 4: Trust**_

When the merchants had spotted her, Clara took a deep, long breath. She was free. Finally free. By now she didn't even care where they were headed, where they would be taking her – she just wanted to go far, far away from everything. Even though the sleeping drought was safely stored inside her pocket Clara had no intention whatsoever of using it. Instead she would tell them about the pirates' plan and make sure they would get a good headstart before nightfall when she was supposed to give the Doctor a sign to board the ship.

And yet Clara couldn't quite shake that nasty feeling of betrayal. The Doctor had been nice to her, he even trusted her enough to send her on this mission and she was about to betray that trust. Why? Clara couldn't say. Maybe it was because she wasn't entirely convinced the Doctor would keep his promise to let her go, maybe it was because they were pirates and they didn't deserve anything else. Even nice pirates were still pirates after all.

A strong hand helped her over the railing and Clara stared into the face of a friendly looking, elderly sailor when she came to stand back on her feet. She had done it. Everything would be fine from now on.

"Thank you so much," she said with a sigh, playing her role like the Doctor had told her to. Only she would play it a little differently, "I thought I was lost. I've been floating around forever."

"My dear, you must be nearly starved," the man said, his voice full of compassion. His tone almost made her feel better about what she was about to do, "But no worries. You're completely safe now. What's your name?"

"Clara," she replied urgently, "But you have to hurry. There are pi-"

" _Clara?_ "

A familiar voice interrupted her and Clara's heart sank immediately. When she turned around she stared right into the face of her husband.

So much for her great escape.

"We've been looking for you for a week," Richard said angrily, raising his voice as he spoke, "Where the hell have you been?"

Clara opened her mouth but no sound came out. She hadn't expected this. She wasn't prepared. Not for her own husband.

"I woke up the morning after our wedding and you were gone, there was no sign of my bride or my father's boat. I was worried sick!"

Clara desperately needed to come up with a story, and she needed to come up with it as quickly as possible. She also needed to decide what she was going to do because going back to her life with Richard was no option for her at all. Clara would rather be back on the pirate ship than anywhere with him.

"Clara, what happened?" he demanded to know.

She took a deep breath. "I was kidnapped. By pirates," she said and it was only half a lie.

" _What?_ "

"I went for a walk after you had gone to sleep to get some fresh air and they snatched me away, stole your father's boat and brought me on board of their ship. Two days ago I managed to get away while they were sleeping."

When Clara stared into Richard's face she thought he couldn't possibly believe her story. She would never believe it herself if someone was telling her this.

To her surprise Richard suddenly stepped closer and placed his arms around her in tight embrace. Clara immediately stiffened under his touch.

"My poor darling," he said. He couldn't really be that stupid, could he? Clara rolled her eyes at the prospect of having to spend another minute in his presence. "I can't even begin to imagine what you must have gone through. But don't you worry. You're safe now. I won't take my eyes off you ever again."

Clara forced a smile when Richard released her from the embrace and suddenly felt the sleeping drought a lot heavier inside her own pocket.

When the sun began to set Clara excused herself to help in the galley, claiming that she was bored out of her mind on this ship. Richard had been so reluctant to let her go but at least her puppy dog eyes worked on him and so she made her way into the galley a few minutes later. The ship's cook however wasn't all too happy about her presence, telling her she would only be in the way.

"Oh, please," she begged him, pouting, "I need something to do. I just want to take my mind off everything that has happened in the last days."

"Fine," he finally sighed and gave in, "You can stir the fish soup but that's it."

Clara smiled at him in relief. "Thank you."

She had made up her mind the moment she had spotted Richard on board of this ship, so she quickly drew the vile from out of her pocket and poured its contents into the soup. Nothing would happen to them, she told herself. They would sleep and wake up to a plundered ship. But they'd be fine.

At dinner time Clara decided to stick to the bread, even though it was dry and stale and when she was asked about it she told everyone that the sea upset her stomach and she was afraid she wouldn't be able to keep her dinner down. Until she realized that Richard wasn't having any of the soup either.

"Why aren't _you_ eating?" she asked him, trying not to show how worried she was about her plan being discovered.

"I've had fish soup for the past week. I can't stand it," Richard replied and took a bite off a slice of bread.

"I've tasted it while I was in the kitchen, it's good," she lied, sipping her drink.

With a sigh Richard reached for his spoon and was about to start eating when the captain suddenly slumped back into his chair. When she looked around the table all the other men were about to fall asleep as well.

"Clara," Richard asked carefully, "What's going on here?"

She took a deep breath before she reached for the holster the man sitting next to her had strapped around his belly and slowly retrieved the pistol.

"I'm sorry," Clara apologized quickly before she swung her warm around and hit Richard right across the head with the handle of the pistol. He fell down onto the floor in an instant.

"Really sorry," she muttered again as she stepped over him and headed outside. Once she had reached the wheel she took a sharp turn around, heading back into the direction they had come from, back to where the Doctor was waiting and then she fired the pistol into the air like he had told her to.

It seemed like an eternity had passed before she could finally spot the sails and she breathed a sigh of relief maybe a moment too soon.

The door swung open and Richard tumbled onto the deck, wearing a look of confusion on his face.

"Clara, what the hell is happening? What have you done?" he demanded to know.

Clara shot around and thought about what she was going to say to him for a long moment. After a while she simply shrugged.

"You should get inside and hide," she nodded towards the TARDIS that was closing in on them, "The pirates will be here any moment."

"Pirates?" Richard asked in disbelief and finally he saw the ship breaking through the darkness, "The pirates that kidnapped you?"

"They didn't kidnap me, they rescued me. _I_ stole the boat and ran away," she said simply.

"But why? Clara, _why_?"

"I don't wanna be with you," Clara shook her head, "But I mean you no harm. Go into your cabin, pretend to be asleep and nothing will happen to you."

The TARDIS had overtaken them and was now turning around. In a few moments the two ships would be head on head and the pirates would start to cross over. Richard should have done like she had told him to but instead he only stared at her quizzically. The she could already hear the voices of the excited pirates and the Doctor swung from one ship to the other on a long rope, landing right next to her.

"Hello," he greeted her with a grin, "Did you miss me?"

Clara laughed but she quickly hid the fact that she did. "Almost," she replied.

"I won't let you take her!" Richard's voice was wavering and he held up both fists, "She is _my_ wife."

The Doctor cocked his head, watching him for a moment until he turned back around to Clara with a frown. "Seriously?"

Clara rolled her eyes.

The Doctor cleared his throat and faced Richard again, chuckling as he did. "Listen, mate. Do you know what we are?"

"You're filthy pirates," he spat in reply.

"That's right. And what do filthy pirates normally do? They take things that don't belong to them," the Doctor explained and suddenly Clara felt his arm around her waist, pulling her to his side, "And I'm taking Clara."

Her first instinct had been to slap him but the expression on Richard's face was well worth letting the Doctor hold her for a few seconds.

"Boys!" the Doctor called for the rest of the crew, "Tie this one to the mast!"

Before Richard could even protest Pit and Johnny had already gotten hold of him and the Doctor led Clara over an improvised bridge back on the TARDIS.

"Did you know Richard would be on that merchant ship?" Clara asked him once her feet were back on the other deck and the Doctor jumped off the railing to join her.

He shrugged in reply. "I had a hunch."

" _How?_ " Clara asked in disbelief. Either the Doctor was truly smart or psychic, "How could you possibly have guessed that? And how did you know I wouldn't double cross you and sail off with the merchants?"

"I didn't know whether you'd betray me. I had certainly hoped you wouldn't but even if," he paused, turning to look back to where the other ship and part of his crew were, taking everything that wasn't nailed down and stuffing it into their own pockets, "I promised to let you go and I won't break that promise."

He turned to look in her direction, his eyes almost boring into her even through the darkness. "As for Richard, it really was just a guess. Cause if you were my wife and you had disappeared, I'd sail the entire world just to find you, too."

Clara opened her mouth to reply but soon realized she that she was lost for words so instead she turned her gaze away and looked straight ahead to where Richard was struggling to free himself from the mast they had tied him to. Poor idiot.


	5. Chapter 5: The Storm

_Thank you all so, so, so, SO much for your sweet reviews. I'm so glad you're loving this story._

 _ **Chapter 5: The Storm**_

The sea smelled different when the Doctor stepped onto the deck that morning and it was almost as if he could feel the charge lying in the air on his skin. They would get rain today, maybe even thunder and he took another deep breath. Yes, most definitely thunder.

He spotted Clara standing at the prow, looking out across the sea and his heart felt a lot heavier than before. He hadn't told her that some time after the encounter with her husband on the merchant ship he had ordered the steersman to turn the ship around and head back to the English coast to Dover. From there Clara would be able to catch transport to London where she had wanted to go and so far the Doctor hadn't had the heart to tell her that. Maybe because a part of him was still hoping she would change her mind and stay.

The Doctor understood all too well why she wouldn't. Clara was a beautiful, young, spirited woman with her whole life ahead of her now that she had managed to dodge her idiot husband. Why on earth would she want to spend her time in the company of a bunch of pirates? He knew why he wanted her to stay and the reasons were as plain as they could possible be. He fancied Clara with her beautiful eyes and her bold nature and having her on board of the TARDIS brightened his days more than he cared to admit to himself. He should tell her about England.

When he came to stand next to Clara and leaned on the railing the Doctor watched her small hands almost caress the crumbling paint.

"She could do with a repaint, you know?"

The Doctor smiled to himself, letting his gaze wander over the waves. The wind had increased since he had stepped outside and the water was turning rougher quickly. Soon they would find themselves in a storm.

"Is it like," Clara paused and suddenly shook her head next to him.

"Like what?" he asked her.

Clara turned around to look straight at him. "An addiction?"

Her question made him chuckle. "Well, you never know something's an addiction until you try to give it up."

"And you never have," Clara sighed and stared straight ahead.

Maybe it was just his own mind playing a trick on him because he so wanted her to stay, but right now he was under the impression that Clara was at least considering it.

"Why would I wanna do that?" he asked her, laughing lightly, "The sea has been my home for as long as I can remember. By now you must have realized that we're not like any other bunch of pirates."

His statement made Clara giggle. "Yeah, you don't actually seem to be doing a lot of pirating."

"I have no interest in violence," he admitted wearily, "I've seen enough of that during my time at the Royal Navy. Most of us have. We're here because we want to be free, because we love the sea. We take what we need and then we move on. I don't think we'll ever stop."

Clara nodded and was about to say something when suddenly they were rudely interrupted by the constantly ill-tempered steersman.

"Captain," he shouted across the deck, "I believe there's a storm coming."

The Doctor turned his head towards the sky and had to agree. The wind was blowing strong and the clouds were racing, turning darker with every passing minute. He guessed that in less than an hour it would be anything but pleasant on deck.

"Is it bad?" Clara asked him.

He smiled down at her. "It could be."

"Are we in danger?"

"Possibly," he replied, "You should wait in your cabin. It's gonna get hectic up here very soon."

"No," Clara said determinedly, "Your crew is as lazy as it gets. You're gonna need every pair of hands you can get."

Her argument made the Doctor laugh. Clara might be many things, but she wasn't a coward. Again he felt like something was stabbed into his chest when he thought about having to let her go soon. "Alright," he agreed eventually, "But don't say I didn't warn you."

 **OOO**

It didn't happen very often but this time the Doctor had greatly underestimated the situation. In less than an hour the sky had darkened to the point where one could almost think it was night, the storm was howling and whipping the sails around and the rain was pouring down mercilessly, flooding the deck and making it more slippery than before. One-eyed Johnny was clawing at the railing of the wavering ship and throwing up into the sea as the waves kept crashing against all sides of the TARDIS. It was as if the sea was toying with them, throwing them around and right now there was no end in sight.

The Doctor looked around and spotted Clara trying to fasten a rope that had come loose from the mast and he dashed across the deck to lend her a helping hand.

"Are you okay?" he yelled across the wind.

"Been better," she replied but she was grinning at him. A part of her seemed to be enjoying it just like he did.

"You could still go to your cabin and wait it out," the Doctor suggested carefully. As much as he loved the fact that she was so fearless and ready to jump right into action, he had seen experienced sailors go over board in this kind of weather and he didn't want her to take unnecessary risks.

"Not gonna happen," Clara replied happily as she finished fastening the rope around the cleat.

When the Doctor thought the storm had been bad before it was only about to grow worse and soon enough the waves were so strong that he struggled to stay on his own two feet. He looked around, searching for Clara and she was holding on tight to the bannister that led up to the wheel. He was about to warn her when he saw it coming, a wave building up and crashing right over the railing, sweeping away everything that wasn't nailed down but when he looked back up Clara was still standing, panting heavily, but still held a tight grip around the wood.

Looking up to the wheel the Doctor couldn't say the same thing about his steersman. The water had knocked him off his feet and before he even had a chance of scrambling back to his feet the next wave came and threw him over board while his screams died out in the storm.

The Doctor ran across the deck to where Clara was standing and grabbed her by the arm. "I need your help," he shouted urgently and dragged her up to the wheel.

"Quick, hold the wheel," he told her and Clara did as she was told while he retrieved a compass from the pocket of his jacket, "I need you to hold this course. Can you do that?"

Clara nodded frantically and the Doctor's gaze again wandered over his ship and his useless crew. Suddenly he wasn't so sure anymore that they were going to make it but he wouldn't allow this kind of thinking to cloud his judgement.

Instead he turned back around to Clara and, without thinking much about it, pressed a kiss to her lips. He had expected a slap in return but instead Clara looked at him in confusion.

"What was that for?" she shouted across the storm.

The Doctor shrugged and couldn't help but smile. "We might all be sent to Davy Jones' locker today. I just wanted to kiss a beautiful woman before I die."

"Better make sure we don't!" Clara told him sternly.

"You probably would have been safer on that merchant ship with your husband than here with us."

Clara fell silent for a long moment and even through the rain he could see her swallow hard before she looked at him determinedly. "I'd rather die a free woman."

"That's the spirit!" he laughed before he ran back down to help the others.

Even though the rain continued like it had before and the crew was still struggling the Doctor thought the storm was beginning to slowly calm down. They had endured the worst and they would endure the rest. Once he had tightened another loose rope back where it belonged he turned around to Clara, who, to his surprise, seemed utterly content at the wheel, steering the TARDIS through the storm. He took a moment to just look at her, standing so proudly behind the wheel that it caused his heart to beat a little faster. Maybe, just maybe, he could convince her to stay. She was so lost in her task that she didn't even notice the boom that had come loose and was now swinging across the deck.

"Clara!" he called out to warn her but it was too late. As the wind shifted it took the boom with it and it struck Clara right across the head before she sank down to the floor.

The Doctor grabbed Johnny's arm as he made his way to her, ordering the boy to take control of the wheel while he knelt down next to Clara and gently lifted her head. She was knocked out but she was breathing. She would be alright.

"My Clara," he whispered, stroking the wet hair out of her face and only now noticed that the rain had stopped, "Clara, you made it. We made it."

The Doctor lifted her up in his arms, determined to carry her inside where it was dry and warm before he turned back to Johnny once more. "Hold our course and we should be in Dover by morning. And make sure the crew doesn't laze around too much."

Johnny nodded and the Doctor turned away, carrying the unconscious Clara safely inside.


	6. Chapter 6: A Queen For A King

_Thank you so, so, so much for the lovely reviews! You don't know how happy they make me!_

 _This is the last chapter for this fic but because you all seem to love Pirate!Twelve so much I have decided to write a sequel which I will be posting right now and it's called "The Last Journey"._

 **Chapter 6: A Queen For A King**

Clara woke up with a start and sat right back up in bed. In her dream she had been at her wedding, saying her vows without ever meaning to keep them and dancing with the man she despised for the simple reason that he was the husband she had never wanted and for a moment she was afraid she was still there, as if her escape had never happened at all. But when she looked up she stared right into the Doctor's face and felt a sudden and strange ease at the sight of him.

"Good morning," he greeted her with a friendly smile, "Or shall I say _good afternoon_? How's the head?"

While the Doctor got up from his chair to sit down next to her, she now realized for the first time that she was in _his_ cabin and not her own. And she also noticed a pain at the back of her head and her hand carefully wandered to the hurting spot.

"Looks like a nasty bump, but you'll be fine," the Doctor concluded after having a look at it. She had so many questions, she wasn't quite sure where to begin.

"What happened?" Clara went for the obvious question first, "Why am I in your cabin?"

"Do you remember the storm?"

Clara nodded carefully.

"You got knocked out by a boom," the Doctor explained calmly, "I brought you here to warm up, you were completely soaked. And I'm afraid the storm damaged one of the windows in your cabin. We'll have to fix that, otherwise it'll be like sleeping in the sea."

Again Clara nodded. She remembered the storm all too well and what the Doctor told her made all the sense in the world until she looked down at herself and noticed the distinct lack of something. She was only wearing her undergarments.

"You undressed me!" Clara almost cried out in horror and reached out to punch him.

"Ow!" the Doctor howled immediately, "Like I said. You were soaked. I didn't want you to catch a cold!"

Clara glared at him but her features soon softened again when she looked into his almost innocent face. For a pirate he was actually quite considerate so she failed to see why she should be too mad at him.

"If it makes you feel better, I tried to be a gentleman," the Doctor said after a moment and when Clara knitted her eyebrows at him the Doctor finally sighed. "Yeah, okay, maybe I could have tried harder."

"You also kissed me," she reminded him.

"Yeah," he admitted after a moment, "Seems like I did. But I thought we were all going to die, so-"

Clara smiled when she bent forward and locked their lips a second time for another, longer kiss. The Doctor seemed about as surprised as she was by her own actions but right now kissing the Doctor was what she wanted. Clara remembered the time when she had wanted nothing more than to leave this ship but since then a lot of things had happened, her fiancé, the storm, all the days she had spent here among them, and now she was even a little sad to leave that behind some day. She only hoped that day wouldn't come too soon because she was beginning to enjoy it.

The Doctor brought his hand to her cheek and pulled her even closer to him and when she opened her mouth and he slid his own tongue inside so deliciously slow she thought she might melt away on the spot.

Gently the Doctor pushed her backwards but as her head landed on the pillow she suddenly winced, breaking their kiss, and sat back up.

"The bump?" the Doctor asked her.

"Yeah," she replied, feeling the spot with her fingers, "Still a little tender."

Clara uttered a small noise of surprise when the Doctor suddenly flipped them over in bed and pulled her on top of him to sit right on his lap. Her surprise didn't last long when he cupped her face in his hands and puller her back down to meet him and Clara was more than willing to let it happen. A part of her might have been reluctant and another part blamed it on sailing around with pirates for too long but since there was no one here to tell her what to do Clara was entirely free to make her own decisions. And at this moment she chose to give herself to the Doctor.

Her hands wandered under his shirt and across his chest that she had seen so many times but never touched. It felt so warm, so smooth under her palm and suddenly she was overcome by the urge to be as close to him as humanly possible. No clothes, just skin on skin and so she broke the kiss to pull his shirt over his head. The Doctor understood quickly as he undressed her and before she knew it she had her wish and Clara landed back on top of him, only too aware of all the places their bodies touched. It made her skin tingle when he leaned forward and brought his mouth to her breast and sucked hard on her sensitive nipple. She inhaled sharply, trying to ignore the burning feeling between her thighs that she got from being so close to him. How was she ever going to leave him after this?

Suddenly the Doctor sat up and pulled her closer to him to kiss her once more. He tasted of all the things she knew she should never want but did and she couldn't help but whimper when she felt his hardness brush against her sex. Right now there was nothing in this world that she wanted more than be one with him, to feel him inside of her but instead of giving in to her the Doctor's lips left hers and trailed down her neck, making her groan in frustration. Instead of waiting for him she finally reached between him and took him into her hand. He was rock solid under her palm and the Doctor moaned when she gave him a couple of strokes.

" _Mhhhhh_ , my Clara," he whispered right as she led him to her entrance and began to lower herself on top of him. Of all the things going through her head when he sank deeper into her Clara couldn't find one word to describe what she was feeling. The Doctor closed his arms around her, pulling her against his own chest and kissed her again. She thought she'd never want to stop kissing him as they began to rock together, trying to find a rhythm.

"My Doctor," she murmured in reply, her breathing becoming faster like the speed of his movements as he thrust up to meet her. She closed her eyes and had to refrain from crying out when suddenly he plunged deeper inside of her, filling her up so completely that it was almost painfully sweet. When he brought his hand between them and slid a finger between her folds Clara found herself grinding against it, the pleasure of it soon becoming so delicious that she found it too much to bear.

She opened her eyes to look at him as the sweat ran over his tattooed hearts and his face was flushed in excitement, his lips parted that she couldn't help but bend down and kiss them. The Doctor moaned into her mouth as she tightened her muscles around him and just when she was about to ask him to go harder, he did, his thrusts becoming faster and more shallow while he was closing in on his orgasm. Clara closed her eyes again, dug her nails into his skin, the feeling of him taking over and soon the waves of her own climax came rolling over her while the Doctor was still inside of her, riding it out until the last second when he finally spilled himself inside of her.

They fell into the cushions, panting heavily and neither of them spoke for a long time because there was absolutely nothing to say that they both didn't already know. Clara wanted for this moment to never end and she knew that the Doctor felt the same way. She just knew it. With a sigh she closed her eyes and leaned against his chest.

Clara stepped out onto the deck the next morning, feeling freer than she ever had before but the sensation fell away from her as soon as she spotted the shore in front of them. The Doctor was intending to keep his promise when she didn't even want him to anymore.

She was only vaguely aware that he came to a halt next to her, also staring at the land that was about to separate them – probably forever.

"I'm a pirate," he began, "But I'm also a man of my word. You're free to go."

"Is that Gijón?" she asked him even though she had recognized the chalk cliffs upon sight.

"No, that's Dover. I told my men to turn around and head back to England," the Doctor explained to her in a calm voice and even though she didn't see his face Clara knew that he was sad.

She turned around to face him.

"Can we go? To Gijón?"

For a moment there was nothing but confusion on the Doctor's face as he was trying to grasp the meaning of her words.

"Are you saying what I hope you're saying?" he asked carefully and Clara giggled.

"Well, you made it sound so interesting and I've always wanted to see the world. I want to see the Spanish dance like the devil. Unless you are still wanted by the Spanish Inquisition?"

"You do know I made that all up, right? I've never actually been to Gijón. Spain, yes, not Gijón," the Doctor admitted after a moment, making it sound as if it should have been obvious.

Clara simply shrugged. "Then I guess it's about time you go."

"About the Inquisition-"

Clara stopped him by placing her index finger over his lips and smiled at him. "Shut up and hoist the sails."

The Doctor grinned at her right before he suddenly reached for her hand and pulled her up to the wheel where he turned towards the crew.

"Gentlemen!" he shouted across the deck, "Hoist the sails! We're going to Gijón!"

 _While the crew cheered the Doctor turned to look at Clara and she smiled back at him, her heart beating fast at the prospect of sailing the seas with the Doctor and she wouldn't stop until she had seen it all. Nothing in this world was ever going to make her leave him._


End file.
